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Guarnacci M, Preiss T. The je ne sais quoi of 5-methylcytosine in messenger RNA. RNA 2024; 30:560-569. [PMID: 38531644 PMCID: PMC11019750 DOI: 10.1261/rna.079982.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
The potential presence of 5-methylcytosine as a sparse internal modification of mRNA was first raised in 1975, and a first map of the modification was also part of the epitranscriptomics "big bang" in 2012. Since then, the evidence for its presence in mRNA has firmed up, and initial insights have been gained into the molecular function and broader biological relevance of 5-methylcytosine when present in mRNA. Here, we summarize the status quo of the field, outline some of its current challenges, and suggest how to address them in future work.
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Affiliation(s)
- Marco Guarnacci
- Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia
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Ortiz-Barahona V, Soler M, Davalos V, García-Prieto CA, Janin M, Setien F, Fernández-Rebollo I, Bech-Serra JJ, De La Torre C, Guil S, Villanueva A, Zhang PH, Yang L, Guarnacci M, Schumann U, Preiss T, Balaseviciute U, Montal R, Llovet JM, Esteller M. Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer. Mol Cancer 2023; 22:83. [PMID: 37173708 PMCID: PMC10176850 DOI: 10.1186/s12943-023-01785-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/08/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND RNA modifications are important regulators of transcript activity and an increasingly emerging body of data suggests that the epitranscriptome and its associated enzymes are altered in human tumors. METHODS Combining data mining and conventional experimental procedures, NSUN7 methylation and expression status was assessed in liver cancer cell lines and primary tumors. Loss-of-function and transfection-mediated recovery experiments coupled with RNA bisulfite sequencing and proteomics determined the activity of NSUN7 in downstream targets and drug sensitivity. RESULTS In this study, the initial screening for genetic and epigenetic defects of 5-methylcytosine RNA methyltransferases in transformed cell lines, identified that the NOL1/NOP2/Sun domain family member 7 (NSUN7) undergoes promoter CpG island hypermethylation-associated with transcriptional silencing in a cancer-specific manner. NSUN7 epigenetic inactivation was common in liver malignant cells and we coupled bisulfite conversion of cellular RNA with next-generation sequencing (bsRNA-seq) to find the RNA targets of this poorly characterized putative RNA methyltransferase. Using knock-out and restoration-of-function models, we observed that the mRNA of the coiled-coil domain containing 9B (CCDC9B) gene required NSUN7-mediated methylation for transcript stability. Most importantly, proteomic analyses determined that CCDC9B loss impaired protein levels of its partner, the MYC-regulator Influenza Virus NS1A Binding Protein (IVNS1ABP), creating sensitivity to bromodomain inhibitors in liver cancer cells exhibiting NSUN7 epigenetic silencing. The DNA methylation-associated loss of NSUN7 was also observed in primary liver tumors where it was associated with poor overall survival. Interestingly, NSUN7 unmethylated status was enriched in the immune active subclass of liver tumors. CONCLUSION The 5-methylcytosine RNA methyltransferase NSUN7 undergoes epigenetic inactivation in liver cancer that prevents correct mRNA methylation. Furthermore, NSUN7 DNA methylation-associated silencing is associated with clinical outcome and distinct therapeutic vulnerability.
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Affiliation(s)
- Vanessa Ortiz-Barahona
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Marta Soler
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Veronica Davalos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Carlos A García-Prieto
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Catalonia, Spain
| | - Maxime Janin
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Fernando Setien
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Irene Fernández-Rebollo
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Joan J Bech-Serra
- Proteomics Unit, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Carolina De La Torre
- Proteomics Unit, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Sonia Guil
- Regulatory RNA and Chromatin Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
- Germans Trias i Pujol Health Science Research Institute, Barcelona, Catalonia, Spain
| | - Alberto Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Pei-Hong Zhang
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Marco Guarnacci
- Shine-Dalgarno Centre for RNA Innovation, Australian National University, Canberra, Australia
| | - Ulrike Schumann
- Shine-Dalgarno Centre for RNA Innovation, Australian National University, Canberra, Australia
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), Queensland, NSW, 2010, Australia
| | - Ugne Balaseviciute
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Catalonia, Spain
| | - Robert Montal
- Hospital Arnau de Vilanova, IRBLleida, University of Lleida (UdL), Catalonia, Spain
| | - Josep M Llovet
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Catalonia, Spain
- ICAHN School of Medicine at Mount Sinai, New York, NY, USA
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, 08010, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, 08010, Spain.
- Centro de Investigacion Biomedica en Red Cancer, Madrid, 28029, Spain.
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, 08907, Spain.
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Rossi F, Centrón-Broco A, Dattilo D, Di Timoteo G, Guarnacci M, Colantoni A, Beltran Nebot M, Bozzoni I. CircVAMP3: A circRNA with a Role in Alveolar Rhabdomyosarcoma Cell Cycle Progression. Genes (Basel) 2021; 12:genes12070985. [PMID: 34203273 PMCID: PMC8303801 DOI: 10.3390/genes12070985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs), a class of covalently closed RNAs formed by a back-splicing reaction, have been involved in the regulation of diverse oncogenic processes. In this article we describe circVAMP3, a novel circular RNA overexpressed in RH4, a representative cell line of alveolar rhabdomyosarcoma. We demonstrated that circVAMP3 has a differential m6A pattern opposed to its linear counterpart, suggesting that the two isoforms can be differently regulated by such RNA modification. Moreover, we show how circVAMP3 depletion in alveolar rhabdomyosarcoma cells can impair cell cycle progression, through the alteration of the AKT-related pathways, pointing to this non-coding RNA as a novel regulator of the alveolar rhabdomyosarcoma progression and as a putative future therapeutic target.
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Affiliation(s)
- Francesca Rossi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy; (F.R.); (A.C.-B.); (D.D.); (G.D.T.); (M.G.); (M.B.N.)
| | - Alvaro Centrón-Broco
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy; (F.R.); (A.C.-B.); (D.D.); (G.D.T.); (M.G.); (M.B.N.)
| | - Dario Dattilo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy; (F.R.); (A.C.-B.); (D.D.); (G.D.T.); (M.G.); (M.B.N.)
| | - Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy; (F.R.); (A.C.-B.); (D.D.); (G.D.T.); (M.G.); (M.B.N.)
| | - Marco Guarnacci
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy; (F.R.); (A.C.-B.); (D.D.); (G.D.T.); (M.G.); (M.B.N.)
| | - Alessio Colantoni
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy;
| | - Manuel Beltran Nebot
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy; (F.R.); (A.C.-B.); (D.D.); (G.D.T.); (M.G.); (M.B.N.)
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy; (F.R.); (A.C.-B.); (D.D.); (G.D.T.); (M.G.); (M.B.N.)
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy;
- Correspondence:
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Di Timoteo G, Dattilo D, Centrón-Broco A, Colantoni A, Guarnacci M, Rossi F, Incarnato D, Oliviero S, Fatica A, Morlando M, Bozzoni I. Modulation of circRNA Metabolism by m 6A Modification. Cell Rep 2021; 31:107641. [PMID: 32402287 DOI: 10.1016/j.celrep.2020.107641] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/24/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) is an RNA modification well-known for its contribution to different processes controlling RNA metabolism, including splicing, stability, and translation of mRNA. Conversely, the role of m6A on the biogenesis and function of circular RNAs (circRNAs) has yet to be addressed. circRNAs belong to a class of covalently closed transcripts produced via a back-splicing reaction whereby a downstream 5' splice donor site fuses to an upstream 3' splice acceptor site. Starting from circ-ZNF609 as a study case, we discover that specific m6As control its accumulation and that METTL3 and YTHDC1 are required to direct the back-splicing reaction. This feature is shared with other circRNAs because we find a significant direct correlation among METTL3 requirement, YTHDC1 binding, and the ability of m6A exons to undergo back-splicing. Finally, because circ-ZNF609 displays the ability to be translated, we show that m6A modifications, through recognition by YTHDF3 and eIF4G2, modulate its translation.
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Affiliation(s)
- Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Dario Dattilo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Alvaro Centrón-Broco
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Marco Guarnacci
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Francesca Rossi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Danny Incarnato
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, the Netherlands
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
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